Last updated on 2026-10-21 05:56:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.3 | 99.36 | 450.20 | 549.56 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.4 | 90.32 | 283.84 | 374.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.4 | 72.00 | 306.22 | 378.22 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.4 | 90.00 | 316.02 | 406.02 | OK | |
| r-devel-windows-x86_64 | 0.1.3 | 127.00 | 2493.00 | 2620.00 | OK | |
| r-patched-linux-x86_64 | 0.1.3 | 110.47 | 436.65 | 547.12 | OK | |
| r-release-linux-x86_64 | 0.1.3 | 111.20 | 435.11 | 546.31 | OK | |
| r-release-macos-arm64 | 0.1.4 | 26.00 | 129.00 | 155.00 | OK | |
| r-release-macos-x86_64 | 0.1.4 | 76.00 | 1106.00 | 1182.00 | OK | |
| r-release-windows-x86_64 | 0.1.4 | 128.00 | 560.00 | 688.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.4 | 31.00 | 375.00 | 406.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.4 | 73.00 | 1072.00 | 1145.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.4 | 141.00 | 638.00 | 779.00 | OK |
Version: 0.1.4
Check: examples
Result: ERROR
Running examples in ‘strollur-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_biom
> ### Title: Create a strollur object from a biom formatted file.
> ### Aliases: read_biom
>
> ### ** Examples
>
>
> if (requireNamespace("h5lite", quietly = TRUE)) {
+ data <- strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom"))
+ data
+ } else {
+ message(paste(
+ "To use this functionality you have to install the",
+ "h5lite package."
+ ))
+ }
HDF5-DIAG: Error detected in HDF5 (2.2.0) thread 1:
#000: src/H5F.c line 575 in H5Fopen(): unable to synchronously open file
major: File accessibility
minor: Unable to open file
#001: src/H5F.c line 555 in H5F__open_api_common(): unable to open file
major: File accessibility
minor: Unable to open file
#002: src/H5VLcallback.c line 2803 in H5VL_file_open(): open failed
major: Virtual Object Layer
minor: Can't open object
#003: src/H5VLcallback.c line 2692 in H5VL__file_open(): open failed
major: Virtual Object Layer
minor: Can't open object
#004: src/H5VLnative_file.c line 69 in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
#005: src/H5Fint.c line 1439 in H5F_open(): can't try opening file
major: File accessibility
minor: Unable to open file
#006: src/H5FD.c line 629 in H5FD_open(): can't open file
major: Virtual File Layer
minor: Unable to open file
#007: src/H5FDsec2.c line 199 in H5FD__sec2_open(): unable to open file: name = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom', errno = 30, error message = 'Read-only file system', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file
Error in h5_create_group(file = file, name = "/") :
Failed to open or create file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
Calls: <Anonymous> ... read_biom_hdf5 -> <Anonymous> -> h5_create_file -> h5_create_group
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [83s/97s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(strollur)
Attaching package: 'strollur'
The following objects are masked from 'package:base':
assign, names, summary
>
> test_check("strollur")
bins is not a valid type for the abundance function. Types include: 'bin', 'sequence', sample' and 'treatment'.
Added 3 sequences.
Added 2425 sequences.
Added 2 resource references.
Added 5 sequences.
> Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: seq5 .
Added 3 sequences.
Added 4 sequences.
Added 2425 sequences.
> Your dataset does not contain sample data, ignoring sample tree.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
> Your tree does not contain a node for every sample in your dataset, ignoring tree. Missing tree nodes for: F3D0, F3D1, F3D141, F3D142, F3D143, F3D144, F3D145, F3D146, F3D147, F3D148, F3D149, F3D150, F3D2, F3D3, F3D5, F3D6, F3D7, F3D8, F3D9 .
Added 3 sequences.
Assigned 3 quality scores.
Assigned 3 sequence abundances.
Assigned 2425 sequence abundances.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bins.
Assigned 171 samples distances.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Assigned 531 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bin taxonomies.
Assigned 2425 asv bins.
Assigned 2425 asv bin taxonomies.
Assigned 63 phylotype bins.
Assigned 63 phylotype bin taxonomies.
Assigned 171 samples distances.
Added 2 resource references.
Added a contigs_report report.
Added a metadata report.
> The table was created with strollur version 0.1.0, which is compatible with the current strollur version: 0.1.2. Converting and importing.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bin taxonomies.
Assigned 2425 asv bins.
Assigned 2425 asv bin taxonomies.
Assigned 63 phylotype bins.
Assigned 63 phylotype bin taxonomies.
Added 2 resource references.
Added a metadata report.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bin taxonomies.
Assigned 2425 asv bins.
Assigned 2425 asv bin taxonomies.
Assigned 63 phylotype bins.
Assigned 63 phylotype bin taxonomies.
Assigned 171 samples distances.
Added 2 resource references.
Added a contigs_report report.
Added a metadata report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bin taxonomies.
Assigned 2425 asv bins.
Assigned 2425 asv bin taxonomies.
Assigned 63 phylotype bins.
Assigned 63 phylotype bin taxonomies.
Assigned 171 samples distances.
Added 2 resource references.
Added a contigs_report report.
Added a metadata report.
Assigned 3 otu bins.
Added 3 sequences.
Assigned 3 sequence abundances.
Assigned 3 otu bins.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
Assigned 531 otu bin taxonomies.
Added 531 sequences.
Assigned 531 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 19 samples to treatments.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
Assigned 531 otu bin taxonomies.
Added 531 sequences.
Assigned 531 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Added 3 sequences.
Assigned 3 quality scores.
Added 3 sequences.
Assigned 3 quality scores.
Assigned 3 sequence abundances.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Assigned 531 otu bin taxonomies.
Assigned 2425 asv bins.
Assigned 2425 asv bin taxonomies.
Assigned 63 phylotype bins.
Assigned 63 phylotype bin taxonomies.
Assigned 171 samples distances.
Added 2 resource references.
Added a contigs_report report.
Added a metadata report.
Added 4 sequences.
Added 1 resource references.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Added 4 sequences.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Added 1 resource references.
Added 2425 sequences.
Added 19 sequences.
> The strollur objects public field 'sequence_tree' are not equivalent.
> The strollur objects public field 'sequence_tree' are not equivalent.
Assigned 531 otu bins.
Assigned 531 otu bins.
> The strollur objects public field 'sample_tree' are not equivalent.
> The strollur objects public field 'sample_tree' are not equivalent.
> The strollur objects public field 'raw' are not equivalent.
The strollur objects have different dataset names.
Added 2425 sequences.
The strollur objects have different sequence data statuses.
Added 2425 sequences.
Assigned 2425 sequence taxonomies.
The strollur objects have different classification statuses.
Assigned 2425 sequence taxonomies.
The strollur objects have different number of unique sequences.
Added 4 sequences.
Added 4 sequences.
The strollur objects include different sequence names.
Added 4 sequences.
Added 4 sequences.
The strollur objects include different sequence strings.
Added 4 sequences.
Added 4 sequences.
The strollur objects include different sequence comments.
Assigned 4 sequence taxonomies.
Assigned 4 sequence taxonomies.
The strollur objects include different sequence taxonomies.
Assigned 2 otu bins.
Added 4 sequences.
The strollur objects include different sequence bin assignment statuses.
Assigned 2 otu bins.
Added 1 resource references.
The strollur objects include different resource_references.
Assigned 4 sequence abundances.
Assigned 4 sequence abundances.
The strollur objects include different sequence abundance data.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Assigned 2 otu bins.
The strollur objects include different bin data.
Added a contigs_report report.
Added 2425 sequences.
The strollur objects include different report data.
Added a metadata report.
The strollur objects include different report data.
Added 4 sequences.
Added 4 sequences.
The strollur objects include different sequence trash codes.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added a contigs_report report.
Added a metadata report.
Added 2 resource references.
starts ends nbases ambigs polymers numns numseqs
Minimum: 1 375 249.0000 0 3.000000 0 1.00
2.5%-tile: 1 375 252.0000 0 4.000000 0 2850.05
25%-tile: 1 375 252.0000 0 4.000000 0 28491.50
Median: 1 375 253.0000 0 4.000000 0 56982.00
75%-tile: 1 375 253.0000 0 5.000000 0 85472.50
97.5%-tile: 1 375 254.0000 0 6.000000 0 111113.95
Maximum: 1 375 256.0000 0 6.000000 0 113963.00
Mean: 1 375 252.7406 0 4.496082 0 56982.00
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added 2425 sequences.
Added 4 sequences.
Added 4 sequences.
Added 4 sequences.
Added 4 sequences.
Added 1 resource references.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin taxonomies.
Assigned 2425 sequence abundances.
Assigned 2425 sequence abundances.
Assigned 2425 sequence abundances.
Assigned 4 sequence abundances.
Assigned 4 sequence abundances.
Assigned 4 sequence abundances.
Assigned 3 otu bins.
Assigned 3 otu bins.
Assigned 3 otu bins.
Assigned 531 otu bins.
Assigned 531 otu bins.
Assigned 4 sequence taxonomies.
Added 1 resource references.
Assigned 4 sequence taxonomies.
Assigned 4 sequence taxonomies.
Assigned 4 sequence taxonomies.
Assigned 2 otu bins.
Assigned 4 otu bins.
Assigned 4 otu bin taxonomies.
Added 1 resource references.
Assigned 4 otu bin taxonomies.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Added a metadata report.
Added a metadata report.
Added 2 resource references.
Added 1 resource references.
Added 2 resource references.
Added a badName report.
Added an align_report report.
Added 2 sequences.
Your report does not contain an entry for every sequence in your dataset, ignoring report.
Added a contigs_report report.
Added a contigs_report report.
Added 2 sequences.
Your report does not contain an entry for every sequence in your dataset, ignoring report.
Added a chimera_report report.
Added a chimera_report report.
Added a contigs_report report.
Added an alignment_report report.
Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
Minimum: 252.0 249 2 251 0.0 0
2.5%-tile: 252.0 249 2 251 0.0 0
25%-tile: 252.0 249 2 251 0.0 0
Median: 253.0 249 2 251 1.0 0
75%-tile: 253.0 249 2 251 2.0 0
97.5%-tile: 253.0 249 2 251 6.5 0
Maximum: 253.0 249 2 251 7.0 0
Mean: 252.6 249 2 251 2.0 0
Expected_Errors
Minimum: 0.002107510
2.5%-tile: 0.002107699
25%-tile: 0.002109400
Median: 0.007777480
75%-tile: 0.025687800
97.5%-tile: 0.027445230
Maximum: 0.027640500
Mean: 0.013064538
QueryLength TemplateLength SearchScore QueryStart QueryEnd
Minimum: 252.0 292.0 57.550 1 252.0
2.5%-tile: 252.0 292.0 58.421 1 252.0
25%-tile: 252.0 292.0 66.260 1 252.0
Median: 253.0 293.0 71.130 1 253.0
75%-tile: 253.0 293.0 74.790 1 253.0
97.5%-tile: 253.0 293.0 81.675 1 253.0
Maximum: 253.0 293.0 82.440 1 253.0
Mean: 252.6 292.6 70.434 1 252.6
TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery
Minimum: 20 271.0 252.0 0
2.5%-tile: 20 271.0 252.0 0
25%-tile: 20 271.0 252.0 0
Median: 20 272.0 253.0 0
75%-tile: 20 272.0 253.0 0
97.5%-tile: 20 272.0 253.0 0
Maximum: 20 272.0 253.0 0
Mean: 20 271.6 252.6 0
GapsInTemplate LongestInsert SimBtwnQuery&Template
Minimum: 0 0 92.060
2.5%-tile: 0 0 92.261
25%-tile: 0 0 94.070
Median: 0 0 94.070
75%-tile: 0 0 96.040
97.5%-tile: 0 0 97.102
Maximum: 0 0 97.220
Mean: 0 0 94.692
Added 4 sequences.
Added 4 sequences.
Added 4 sequences.
> Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: seq4 .
Added 2425 sequences.
Added 4 sequences.
> Your dataset does not contain sample data, ignoring sample tree.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
> Your tree does not contain a node for every sample in your dataset, ignoring tree. Missing tree nodes for: F3D0, F3D1, F3D141, F3D142, F3D143, F3D144, F3D145, F3D146, F3D147, F3D148, F3D149, F3D150, F3D2, F3D3, F3D5, F3D6, F3D7, F3D8, F3D9 .
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
data frame with 0 columns and 0 rows
data frame with 0 columns and 0 rows
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence taxonomies.
Assigned 2425 sequence taxonomies.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 2425 sequence taxonomies.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin representative sequences.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Added 4 sequences.
Added 2 sequences.
Added 3 sequences.
Assigned 3 quality scores.
Added 3 sequences.
Assigned 3 quality scores.
Assigned 531 otu bins.
Assigned 171 samples distances.
Added 1 resource references.
Added 1 sequences.
Added 2425 sequences.
Added 2425 sequences.
Added 3 sequences.
Assigned 3 otu bins.
Assigned 3 otu bins.
Assigned 3 otu bins.
Assigned 3 otu bins.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Assigned 4 sequence abundances.
Assigned 2 sequence abundances.
Assigned 4 sequence taxonomies.
Assigned 4 sequence abundances.
Assigned 3 samples to treatments.
Assigned 4 sequence abundances.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Assigned 3 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 4 sequence taxonomies.
Assigned 3 otu bins.
Assigned 4 sequence taxonomies.
HDF5-DIAG: Error detected in HDF5 (2.2.0) thread 1:
#000: src/H5F.c line 575 in H5Fopen(): unable to synchronously open file
major: File accessibility
minor: Unable to open file
#001: src/H5F.c line 555 in H5F__open_api_common(): unable to open file
major: File accessibility
minor: Unable to open file
#002: src/H5VLcallback.c line 2803 in H5VL_file_open(): open failed
major: Virtual Object Layer
minor: Can't open object
#003: src/H5VLcallback.c line 2692 in H5VL__file_open(): open failed
major: Virtual Object Layer
minor: Can't open object
#004: src/H5VLnative_file.c line 69 in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
#005: src/H5Fint.c line 1439 in H5F_open(): can't try opening file
major: File accessibility
minor: Unable to open file
#006: src/H5FD.c line 629 in H5FD_open(): can't open file
major: Virtual File Layer
minor: Unable to open file
#007: src/H5FDsec2.c line 199 in H5FD__sec2_open(): unable to open file: name = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom', errno = 30, error message = 'Read-only file system', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file
Saving _problems/test-read_biom-7.R
Added 100 sequences.
Assigned 100 sequence abundances.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Added 6 sequences.
Assigned 6 sequence abundances.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Assigned 531 asv bins.
Assigned 531 phylotype bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bins.
Assigned 531 otu bins.
Added 591 sequences.
Assigned 591 sequence abundances.
Added 531 sequences.
Assigned 531 sequence abundances.
Assigned 531 sequence taxonomies.
Added a metadata report.
Added 759 sequences.
Assigned 759 sequence abundances.
Assigned 759 asv bins.
Assigned 759 asv bin taxonomies.
Added a contigs_report report.
Added 3 sequences.
Added 3 sequences.
Added 2425 sequences.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
starts ends nbases ambigs polymers numns numseqs
Minimum: 1 375 249.0000 0 3.000000 0 1.000
2.5%-tile: 1 375 252.0000 0 4.000000 0 2695.275
25%-tile: 1 375 252.0000 0 4.000000 0 26943.750
Median: 1 375 253.0000 0 4.000000 0 53886.500
75%-tile: 1 375 253.0000 0 5.000000 0 80829.250
97.5%-tile: 1 375 254.0000 0 6.000000 0 105077.725
Maximum: 1 375 256.0000 0 6.000000 0 107772.000
Mean: 1 375 252.7345 0 4.493546 0 53886.500
Added 1 sequences.
starts ends nbases ambigs polymers numns numseqs
Minimum: 1 253 253 0 4 0 1
2.5%-tile: 1 253 253 0 4 0 1
25%-tile: 1 253 253 0 4 0 1
Median: 1 253 253 0 4 0 1
75%-tile: 1 253 253 0 4 0 1
97.5%-tile: 1 253 253 0 4 0 1
Maximum: 1 253 253 0 4 0 1
Mean: 1 253 253 0 4 0 1
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Assigned 531 otu bins.
Added 3 sequences.
Assigned 3 quality scores.
Assigned 531 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/ (stored 0%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.shared (deflated 89%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.shared (deflated 67%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.design (deflated 65%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.fasta (deflated 92%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.resource_reference (deflated 43%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.metadata (deflated 48%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.cons.taxonomy (deflated 85%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.cons.taxonomy (deflated 96%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.list (deflated 83%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.sequence.tree (deflated 77%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.sample.tree (deflated 57%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.list (deflated 82%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.list (deflated 82%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.cons.taxonomy (deflated 95%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.taxonomy (deflated 91%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.count_table (deflated 81%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.shared (deflated 79%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.contigs_report (deflated 81%)
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added 2 resource references.
Added a metadata report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/ (stored 0%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.shared (deflated 89%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.shared (deflated 67%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.design (deflated 65%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.cons.taxonomy (deflated 85%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.cons.taxonomy (deflated 96%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.phylotype.list (deflated 83%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.asv.list (deflated 82%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.list (deflated 82%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.cons.taxonomy (deflated 95%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.count_table (deflated 81%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/miseq_sop.otu.shared (deflated 79%)
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Added an alignment_report report.
Added a contigs_report report.
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/ (stored 0%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/strollur.1792522898.contigs_report (deflated 44%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/strollur.1792522898.alignment_report (deflated 57%)
Added an alignment_report report.
Added a contigs_report report.
Added a chimera_report report.
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/ (stored 0%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/strollur.1792522899.chimera_report (deflated 82%)
adding: home/hornik/tmp/scratch/RtmpOTCVdE/tmp/strollur.1792522899.count_table (deflated 79%)
Added a chimera_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Added 6 sequences.
Assigned 6 sequence abundances.
Added 6 sequences.
Assigned 6 sequence abundances.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
Assigned 531 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 531 sequences.
Assigned 531 sequence abundances.
Assigned 531 sequence taxonomies.
Added 19216 sequences.
Assigned 19216 sequence abundances.
Assigned 19216 sequence taxonomies.
Added a metadata report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Added a metadata report.
Assigned 19 samples to treatments.
Added 3 sequences.
Assigned 3 quality scores.
Assigned 531 otu bins.
Added 2425 sequences.
Assigned 2425 sequence abundances.
Assigned 2425 sequence taxonomies.
Assigned 531 otu bins.
Assigned 2425 asv bins.
Assigned 63 phylotype bins.
Assigned 19 samples to treatments.
Assigned 171 samples distances.
Assigned 531 otu bin taxonomies.
Assigned 531 otu bin representative sequences.
Added a metadata report.
Added 2 resource references.
Added a contigs_report report.
Assigned 531 otu bins.
Added 2425 sequences.
Added 2 resource references.
Added 2425 sequences.
Added an align_report report.
Added 4 sequences.
Assigned 531 otu bins.
Assigned 2 otu bins.
Assigned 2 otu bin representative sequences.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Assigned 4 sequence abundances.
Assigned 4 sequence taxonomies.
Assigned 4 sequence taxonomies.
Assigned 531 otu bins.
Assigned 19 samples to treatments.
Assigned 531 otu bins.
Assigned 531 otu bin taxonomies.
Assigned 4 sequence abundances.
Added 3 sequences.
Added 1 sequences.
Added 4 sequences.
Assigned 4 sequence abundances.
Added 4 sequences.
Assigned 4 sequence abundances.
Assigned 10 sequence abundances.
Assigned 2 otu bins.
Added 1 resource references.
Assigned 2 otu bin representative sequences.
The dataset already contains a resource_reference named 'myReference', overwriting existing reference.
Added 1 resource references.
Assigned 4 otu bins.
Assigned 3 otu bins.
type trash_code unique total
1 sequence test 1 13
Assigned 10 sequence abundances.
type trash_code unique total
1 sequence test 1 15
Assigned 3 otu bins.
Added 4 sequences.
Assigned 4 sequence abundances.
Assigned 3 otu bins.
Assigned 6 samples to treatments.
Assigned 6 samples to treatments.
non_existant_otu is not in your dataset, ignoring.
type trash_code unique total
1 sequence bad_bin 3 30
2 otu bad_bin 1 30
Assigned 4 sequence taxonomies.
Added 2 sequences.
seq3 is not in your dataset, ignoring.
seq4 is not in your dataset, ignoring.
Assigned 2 sequence taxonomies.
Assigned 4 sequence taxonomies.
Assigned 4 sequence abundances.
Assigned 2 otu bins.
Assigned 2 otu bins.
Assigned 2 otu bin taxonomies.
Assigned 2 otu bin taxonomies.
Added an align_report report.
Added 1 resource references.
Added 3 sequences.
Assigned 3 quality scores.
Added 1 resource references.
Added 3 sequences.
Assigned 531 otu bins.
Assigned 171 samples distances.
Added 1 resource references.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-r6_strollur.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read_biom.R:7:3'): read_biom ───────────────────────────────────
Error in `h5_create_group(file = file, name = "/")`: Failed to open or create file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
Backtrace:
▆
1. └─strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom")) at test-read_biom.R:7:3
2. └─rbiom::read_biom(biom)
3. └─rbiom:::read_biom_hdf5(fp)
4. └─h5lite::h5_open(file = fp)
5. └─h5lite::h5_create_file(file)
6. └─h5lite::h5_create_group(file = file, name = "/")
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc